ArticleMolecular ecology2014
Testing models of speciation from genome sequences: divergence and asymmetric admixture in Island South-East Asian Sus species during the Plio-Pleistocene climatic fluctuations.
Article in Molecular ecology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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17 citing papers in PubMed.
- The 1000 Chinese Indigenous Pig Genomes Project provides insights into the genomic architecture of pigs.Nature communications · 2024Article
- Swine global genomic resources: insights into wild and domesticated populations.Mammalian genome : official journal of the International Mammalian Genome Society · 2023Article
- Graph-based algorithms for Laplace transformed coalescence time distributions.PLoS computational biology · 2022Article
- The Visayan Warty Pig (Sus cebifrons) Genome Provides Insight Into Chromosome Evolution and Sensory Adaptation in Pigs.Molecular biology and evolution · 2022Article
- Distinct traces of mixed ancestry in western commercial pig genomes following gene flow from Chinese indigenous breeds.Frontiers in genetics · 2022Article
- Selection and isolation define a heterogeneous divergence landscape between hybridizing Heliconius butterflies.Evolution; international journal of organic evolution · 2021Article
- Unlocking the origins and biology of domestic animals using ancient DNA and paleogenomics.BMC biology · 2019Review
- Genomic analysis on pygmy hog reveals extensive interbreeding during wild boar expansion.Nature communications · 2019Article
- ABLE: blockwise site frequency spectra for inferring complex population histories and recombination.Genome biology · 2018Article
- Evidence of evolutionary history and selective sweeps in the genome of Meishan pig reveals its genetic and phenotypic characterization.GigaScience · 2018Article
- Population-genomic inference of the strength and timing of selection against gene flow.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- Denisovans, Melanesians, Europeans, and Neandertals: The Confusion of DNA Assumptions and the Biological Species Concept.Journal of molecular evolution · 2016Article
- A genomic perspective on hybridization and speciation.Molecular ecology · 2016Review
- A decade of pig genome sequencing: a window on pig domestication and evolution.Genetics, selection, evolution : GSE · 2016Review
- Article
- Evidence of long-term gene flow and selection during domestication from analyses of Eurasian wild and domestic pig genomes.Nature genetics · 2015Article
- Using targeted enrichment of nuclear genes to increase phylogenetic resolution in the neotropical rain forest genus Inga (Leguminosae: Mimosoideae).Frontiers in plant science · 2015Article
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5 authors.
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Abstract
In many temperate regions, ice ages promoted range contractions into refugia resulting in divergence (and potentially speciation), while warmer periods led to range expansions and hybridization. However, the impact these climatic oscillations had in many parts of the tropics remains elusive. Here, we investigate this issue using genome sequences of three pig (Sus) species, two of which are found on islands of the Sunda-shelf shallow seas in Island South-East Asia (ISEA). A previous study revealed signatures of interspecific admixture between these Sus species (Genome biology, 14, 2013, R107). However, the timing, directionality and extent of this admixture remain unknown. Here, we use a likelihood-based model comparison to more finely resolve this admixture history and test whether it was mediated by humans or occurred naturally. Our analyses suggest that interspecific admixture between Sunda-shelf species was most likely asymmetric and occurred long before the arrival of humans in the region. More precisely, we show that these species diverged during the late Pliocene but around 23% of their genomes have been affected by admixture during the later Pleistocene climatic transition. In addition, we show that our method provides a significant improvement over D-statistics which are uninformative about the direction of admixture.
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